Align 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-) (characterized)
to candidate Pf1N1B4_2275 Fumarylacetoacetate hydrolase family protein
Query= reanno::BFirm:BPHYT_RS34210 (282 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2275 Length = 221 Score = 115 bits (289), Expect = 6e-31 Identities = 68/183 (37%), Positives = 100/183 (54%), Gaps = 5/183 (2%) Query: 70 IGKFICIGLNYADHAAESNLPVPAEPVIFNKWTSAISGPNDDVEIPRGSKKTDWEVELGV 129 +GK +CIG NYA+HA E + PVP EP++F K S + IP +E E+ V Sbjct: 17 LGKVVCIGRNYAEHAKELDNPVPTEPLLFIKPGSCVVPLEGGFSIPTERGSVHYEAEIAV 76 Query: 130 VIGKP-AKYIDEANALDYVAGYCVINDVSEREWQIE---KGGTWDKGKGFDTFGPIGPWV 185 +IGKP + LD ++G D++ R+ Q E KG W+ K FD I P+ Sbjct: 77 LIGKPLSTKPSREEVLDAISGIAPALDLTLRDKQAELKAKGLPWEIAKSFDGAAVIAPF- 135 Query: 186 VTRDEVADPQNLSLWLEVDGHRYQNGSTKTMVFGVAKLVSYVSQCMSLQPGDVISTGTPP 245 V AD ++ + L ++G Q+G++K M+ + ++ Y++ C SLQ GDVI TGTP Sbjct: 136 VAGSTFADLTDIGIRLTINGEVRQDGNSKDMLNPIVPMIQYMAGCFSLQAGDVILTGTPV 195 Query: 246 GVG 248 GVG Sbjct: 196 GVG 198 Lambda K H 0.315 0.138 0.422 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 230 Number of extensions: 13 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 282 Length of database: 221 Length adjustment: 24 Effective length of query: 258 Effective length of database: 197 Effective search space: 50826 Effective search space used: 50826 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory